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Fix duplicate metabolites identified by ChEBI IDs(2) #667

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merged 3 commits into from
Jun 25, 2023
Merged

Fix duplicate metabolites identified by ChEBI IDs(2) #667

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e3d758e
fix-change ChEBI ID annotations
JHL-452b Jun 25, 2023
7436a50
fix-replace mets
JHL-452b Jun 25, 2023
954fe1a
Merge branch 'develop' into pr/667
feiranl Jun 25, 2023
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3 changes: 2 additions & 1 deletion data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Expand Up @@ -2211,4 +2211,5 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM03325c" "MAM03325" "C08276" "C08276" "HMDB0001527" "CHEBI:1438" "563" "" "" "" "C08276" "MNXM2782" "" "C08276_c"
"MAM00591c" "MAM00591" "" "C14748" "" "CHEBI:34306" "" "" "" "HC02179" "" "MNXM6760" "m00591c" "m00591c"
"MAM00591e" "MAM00591" "" "C14748" "" "CHEBI:34306" "" "" "" "HC02179" "" "MNXM6760" "m00591s" "m00591s"
"MAM03162c" "MAM03162" "" "C05578" "" "CHEBI:27404" "" "" "" "" "M03162" "MNXM2336" "m03162c" "m03162c"
"MAM03162c" "MAM03162" "" "C05578" "" "CHEBI:27404" "" "" "" "" "M03162" "MNXM2336" "m03162c" "m03162c"
"MAM03231c" "MAM03231" "" "" "" "CHEBI:57277" "" "" "" "" "3hppa" "" "" "3hppa_c"
12 changes: 2 additions & 10 deletions model/Human-GEM.yml
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Expand Up @@ -4,7 +4,7 @@
short_name: "Human-GEM"
full_name: "Generic genome-scale metabolic model of Homo sapiens"
version: ""
date: "2023-06-21"
date: "2023-06-25"
taxonomy: "9606"
github: "https://github.com/SysBioChalmers/Human-GEM"
description: "Genome-scale metabolic models are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. This is the latest version of Human-GEM, which is a genome-scale metabolic model of a generic human cell. The objective of Human-GEM is to serve as a community model for enabling integrative and mechanistic studies of human metabolism."
Expand Down Expand Up @@ -54953,14 +54953,6 @@
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03231c"
- name: "3-Hydroxyphenylpropionic Acid (3-Hppa)"
- compartment: "c"
- formula: "C9H9O3"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM02622e"
- name: "normetanephrine"
Expand Down Expand Up @@ -257112,8 +257104,8 @@
- id: "MAR10470"
- name: "3-Hydroxyphenylpropionic Acid Uptake"
- metabolites: !!omap
- MAM03231c: 1
- MAM03231e: -1
- MAM03232c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
Expand Down
21 changes: 10 additions & 11 deletions model/metabolites.tsv
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Expand Up @@ -3538,7 +3538,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02041e" "MAM02041" "h2o2" "C00027" "HMDB0003125" "CHEBI:16240" "784" "" "" "HC00036" "h2o2" "MNXM22" "m02041s" "m02041s"
"MAM02042c" "MAM02042" "" "C00283" "" "CHEBI:16136" "402" "" "" "HC00250" "HC00250" "MNXM162964;MNXM89582" "m02042c" "m02042c"
"MAM02042e" "MAM02042" "" "C00283" "" "CHEBI:16136" "402" "" "" "HC00250" "HC00250" "MNXM162964;MNXM89582" "m02042s" "m02042s"
"MAM02043c" "MAM02043" "" "C05529" "" "CHEBI:16094" "24478" "" "" "HC01501" "HC01501" "MNXM164836;MNXM323" "m02043c" "m02043c"
"MAM02043c" "MAM02043" "" "C05529" "" "CHEBI:5587" "24478" "" "" "HC01501" "HC01501" "MNXM164836;MNXM323" "m02043c" "m02043c"
"MAM02044c" "MAM02044" "" "" "" "" "" "PROTEIN" "" "HC01939" "HC01939" "" "m02044c" "m02044c"
"MAM02044l" "MAM02044" "" "" "" "" "" "PROTEIN" "" "HC01939" "HC01939" "" "m02044l" "m02044l"
"MAM02044e" "MAM02044" "" "" "" "" "" "PROTEIN" "" "HC01939" "HC01939" "" "m02044s" "m02044s"
Expand Down Expand Up @@ -4411,9 +4411,9 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02578x" "MAM02578" "" "C00014" "" "CHEBI:16134" "" "" "" "HC00024" "" "" "m02578p" "m02578p"
"MAM02578r" "MAM02578" "" "C00014" "" "CHEBI:16134" "" "" "" "HC00024" "" "" "m02578r" "m02578r"
"MAM02578e" "MAM02578" "" "C00014" "" "CHEBI:16134" "" "" "" "HC00024" "" "" "m02578s" "m02578s"
"MAM02579c" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:16134" "222" "" "" "HC00765" "nh4" "MNXM15" "m02579c" "m02579c"
"MAM02579m" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:16134" "222" "" "" "HC00765" "nh4" "MNXM15" "m02579m" "m02579m"
"MAM02579e" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:16134" "222" "" "" "HC00765" "nh4" "MNXM15" "m02579s" "m02579s"
"MAM02579c" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:28938" "222" "" "" "HC00765" "nh4" "MNXM15" "m02579c" "m02579c"
"MAM02579m" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:28938" "222" "" "" "HC00765" "nh4" "MNXM15" "m02579m" "m02579m"
"MAM02579e" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:28938" "222" "" "" "HC00765" "nh4" "MNXM15" "m02579s" "m02579s"
"MAM02580c" "MAM02580" "" "C14789" "" "" "" "" "" "" "M02580" "MNXM7572" "m02580c" "m02580c"
"MAM02581c" "MAM02581" "nmn" "C00455" "HMDB0000229" "CHEBI:16171" "14180" "" "" "HC00366" "nmn" "MNXM355" "m02581c" "m02581c"
"MAM02581m" "MAM02581" "nmn" "C00455" "HMDB0000229" "CHEBI:16171" "14180" "" "" "HC00366" "nmn" "MNXM355" "m02581m" "m02581m"
Expand Down Expand Up @@ -5572,7 +5572,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM00809r" "MAM00809" "4mzym_int2" "C15816" "" "CHEBI:50593" "" "LMST01010167" "" "HC02109" "4mzym_int2" "MNXM162901;MNXM36392;MNXM8744" "" "m00809r"
"MAM04082r" "MAM04082" "zym_int2" "" "" "" "22298942" "" "" "" "zym_int2" "MNXM97119" "" "zym_int2_r"
"MAM03158r" "MAM03158" "zymst" "C05437" "" "CHEBI:18252" "92746" "LMST01010066" "" "HC01451" "zymst" "MNXM574" "" "m03158r"
"MAM02579r" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:16134" "222" "" "" "HC00765" "nh4" "MNXM15" "" "m02579r"
"MAM02579r" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:28938" "222" "" "" "HC00765" "nh4" "MNXM15" "" "m02579r"
"MAM01427m" "MAM01427" "cdpdag_hs" "C00269" "" "" "" "LMGP13010000" "" "HC02078" "cdpdag_hs" "MNXM5661" "" "m01427m"
"MAM02733m" "MAM02733" "pa_hs" "C00416" "" "CHEBI:16337" "" "LMGP10010000" "" "HC02049" "pa_hs" "MNXM77635" "" "m02733m"
"MAM00121x" "MAM00121" "clpndcoa" "C16166" "HMDB0006267" "CHEBI:63541" "53477812" "LMFA07050048" "CE4822" "" "clpndcoa" "MNXM4529;MNXM97364" "" "m00121p"
Expand All @@ -5585,11 +5585,11 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM01431e" "MAM01431" "crmp_hs" "" "" "" "" "" "" "HC02165" "crmp_hs" "MNXM92165" "" "m01431s"
"MAM00950x" "MAM00950" "dmnoncrn" "" "" "" "" "" "" "" "dmnoncrn" "MNXM8138" "" "m00950p"
"MAM03554x" "MAM03554" "dmnoncoa" "" "" "" "" "" "" "" "dmnoncoa" "MNXM6100" "" "dmnoncoa_p"
"MAM02579n" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:16134" "222" "" "" "HC00765" "nh4" "MNXM15" "" "m02579n"
"MAM02579n" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:28938" "222" "" "" "HC00765" "nh4" "MNXM15" "" "m02579n"
"MAM00240r" "MAM00240" "dag_hs" "C00641" "" "CHEBI:17815" "" "LMGL02010000" "" "HC02055" "dag_hs" "MNXM59" "" "m00240r"
"MAM02733n" "MAM02733" "pa_hs" "C00416" "" "CHEBI:16337" "" "LMGP10010000" "" "HC02049" "pa_hs" "MNXM77635" "" "m02733n"
"MAM00240e" "MAM00240" "dag_hs" "C00641" "" "CHEBI:17815" "" "LMGL02010000" "" "HC02055" "dag_hs" "MNXM59" "" "m00240s"
"MAM02579x" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:16134" "222" "" "" "HC00765" "nh4" "MNXM15" "" "m02579p"
"MAM02579x" "MAM02579" "nh4" "C01342" "HMDB0000051" "CHEBI:28938" "222" "" "" "HC00765" "nh4" "MNXM15" "" "m02579p"
"MAM02959c" "MAM02959" "tag_hs" "C00422" "" "CHEBI:17855" "" "LMGL03010000" "" "HC02062" "tag_hs" "MNXM9170" "" "m02959c"
"MAM01449r" "MAM01449" "zymstnl" "C03845" "HMDB0006841" "CHEBI:16608" "101770" "LMST01010096" "" "HC02126" "zymstnl" "MNXM2494" "" "m01449r"
"MAM01066r" "MAM01066" "chlstol" "C05439" "" "CHEBI:16290" "" "" "" "HC01452" "chlstol" "MNXM162749;MNXM830" "" "m01066r"
Expand Down Expand Up @@ -5698,7 +5698,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02733g" "MAM02733" "pa_hs" "C00416" "" "CHEBI:16337" "" "LMGP10010000" "" "HC02049" "pa_hs" "MNXM77635" "" "m02733g"
"MAM02684m" "MAM02684" "pchol_hs" "C00157" "" "CHEBI:16110" "" "" "" "HC02000" "pchol_hs" "MNXM2028" "" "m02684m"
"MAM03850r" "MAM03850" "pecgoncoa" "" "" "" "443846" "" "" "" "pecgoncoa" "MNXM92624" "" "pecgoncoa_r"
"MAM03887x" "MAM03887" "pristcoa" "" "" "CHEBI:64039" "25137904" "" "" "" "pristcoa" "MNXM7699" "" "pristcoa_p"
"MAM03887x" "MAM03887" "pristcoa" "" "" "CHEBI:77250" "25137904" "" "" "" "pristcoa" "MNXM7699" "" "pristcoa_p"
"MAM02717c" "MAM02717" "pgp_hs" "C03892" "" "" "" "LMGP05010000" "" "HC02095" "pgp_hs" "MNXM12647" "" "m02717c"
"MAM02725m" "MAM02725" "phpyr" "C00166" "HMDB0000205" "CHEBI:30851" "997" "" "" "" "phpyr" "MNXM162242;MNXM210" "" "m02725m"
"MAM00553r" "MAM00553" "pail4p_hs" "C01277" "" "CHEBI:17526" "" "" "" "" "pail4p_hs" "MNXM2456" "" "m00553r"
Expand Down Expand Up @@ -6486,7 +6486,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02741e" "MAM02741" "pan4p" "C01134" "" "CHEBI:16858" "987" "" "" "HC00681" "pan4p" "MNXM373" "" "m02741s"
"MAM03933e" "MAM03933" "slfcys" "C05824" "HMDB0000731" "CHEBI:27891" "115015" "" "" "" "slfcys" "MNXM2428" "" "slfcys_s"
"MAM01828e" "MAM01828" "fmn" "C00061" "HMDB0001520" "CHEBI:17621" "643976" "" "" "HC00064" "fmn" "MNXM119" "" "m01828s"
"MAM02679e" "MAM02679" "ptth" "C00831" "HMDB0003426" "CHEBI:15525" "15667" "" "" "HC00554" "ptth" "MNXM1154" "" "m02679s"
"MAM02679e" "MAM02679" "ptth" "C00154" "HMDB0003426" "CHEBI:16753" "15667" "" "" "HC00554" "ptth" "MNXM1154" "" "m02679s"
"MAM03102e" "MAM03102" "q10h2" "C00390" "" "CHEBI:17976" "9962735" "" "" "HC00324" "q10h2" "MNXM9200" "" "m03102s"
"MAM02439x" "MAM02439" "mal__L" "C00149" "HMDB0000156" "CHEBI:30797" "222656" "" "" "HC00146" "mal_L" "MNXM98" "" "m02439p"
"MAM03933c" "MAM03933" "slfcys" "C05824" "HMDB0000731" "CHEBI:27891" "115015" "" "" "" "slfcys" "MNXM2428" "" "slfcys_c"
Expand Down Expand Up @@ -6703,7 +6703,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM00784e" "MAM00784" "3hmp" "C06001" "HMDB0000023" "CHEBI:37373" "440873" "" "" "HC00705" "3hmp" "MNXM396" "" "m00784s"
"MAM03234c" "MAM03234" "3hpppnohgluc" "" "" "" "" "" "" "" "3hpppnohgluc" "" "" "3hpppnohgluc_c"
"MAM03234e" "MAM03234" "3hpppnohgluc" "" "" "" "" "" "" "" "3hpppnohgluc" "" "" "3hpppnohgluc_s"
"MAM03232c" "MAM03232" "3hpppn" "" "" "CHEBI:57277" "" "" "" "" "3hpppn" "MNXM1634" "" "3hpppn_c"
"MAM03232c" "MAM03232" "3hpppn" "" "" "CHEBI:57277" "" "" "" "" "3hpppn" "MNXM1634" "" "3hpppn_c;MAM03231c"
"MAM03233c" "MAM03233" "3hpppnoh" "" "" "" "" "" "" "" "3hpppnoh" "" "" "3hpppnoh_c"
"MAM02142e" "MAM02142" "3hpp" "C01013" "HMDB0000700" "CHEBI:33404" "68152" "" "" "HC00625" "3hpp" "MNXM872" "" "m02142s"
"MAM03247e" "MAM03247" "3mhis" "" "" "CHEBI:70959" "" "" "" "" "3mhis" "" "" "3mhis_s"
Expand Down Expand Up @@ -6867,7 +6867,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM03215e" "MAM03215" "3hcinnm" "" "" "" "" "" "" "" "3hcinnm" "MNXM1799" "" "3hcinnm_s"
"MAM03215c" "MAM03215" "3hcinnm" "" "" "" "" "" "" "" "3hcinnm" "MNXM1799" "" "3hcinnm_c"
"MAM03231e" "MAM03231" "" "" "" "" "" "" "" "" "3hppa" "" "" "3hppa_s"
"MAM03231c" "MAM03231" "" "" "" "CHEBI:57277" "" "" "" "" "3hppa" "" "" "3hppa_c"
"MAM02622e" "MAM02622" "normete__L" "C05589" "HMDB0000819" "CHEBI:144308" "1237" "" "" "" "normete_L" "MNXM3674" "" "m02622s"
"MAM00400e" "MAM00400" "" "C05300" "HMDB0000335" "CHEBI:776" "115116" "LMST02010041" "" "" "C05300" "MNXM3794" "" "m00400s"
"MAM01698e" "MAM01698" "dhbpt" "C00268" "" "" "1879" "" "" "HC00242" "dhbpt" "MNXM162257;MNXM90267" "" "m01698s"
Expand Down